From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 1 Sep 2015 12:47:37 +0000 (+0100)
Subject: JAL-1672 additional assertions added
X-Git-Tag: Release_2_10_0~511^2~10
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bed7b4223494ebb85d7ddf9e20b5a01bc3355504;p=jalview.git

JAL-1672 additional assertions added
---

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index d9b1d90..1171bfd 100644
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -28,6 +28,9 @@ import jalview.analysis.CrossRef;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
 
@@ -62,6 +65,11 @@ public class DbRefFetcherTest
   {
   }
 
+  /**
+   * Tests that standard protein database sources include Uniprot (as the first)
+   * and also PDB. (Additional sources are dependent on available of DAS
+   * services.)
+   */
   @Test(groups ={ "Functional" })
   public void testStandardProtDbs()
   {
@@ -77,38 +85,53 @@ public class DbRefFetcherTest
         srces.addAll(srcesfordb);
       }
     }
-    DbSourceProxy uniprot = null;
+
     int i = 0;
+    int uniprotPos = -1;
+    int pdbPos = -1;
     // append the selected sequence sources to the default dbs
     for (DbSourceProxy s : srces)
     {
-      if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+      if (s instanceof jalview.ws.dbsources.Uniprot)
       {
-        i++;
+        uniprotPos = i;
       }
-
-      if (s instanceof jalview.ws.dbsources.Uniprot)
+      if (s instanceof jalview.ws.dbsources.Pdb)
       {
-        uniprot = s;
-        break;
+        pdbPos = i;
       }
+      i++;
     }
 
     assertTrue("Failed to find Uniprot source as first source amongst "
-            + srces.size() + " sources (source was at position " + i + ")",
-            uniprot != null && i < 2);
+            + srces.size() + " sources (source was at position "
+            + uniprotPos + ")", uniprotPos == 0);
+    assertTrue("Failed to find PDB source amongst " + srces.size()
+            + " sources", pdbPos >= 0);
   }
 
+  /**
+   * Tests retrieval of one entry from EMBL. Test is dependent on availability
+   * of network and the EMBL service.
+   * 
+   * @throws Exception
+   */
   @Test(groups =
   { "External" })
   public void testEmblUniprotProductRecovery() throws Exception
   {
-    String retrievalId = "CAA23748"; // "V00488";
+    String retrievalId = "V00488";
     DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
     assertNotNull("Couldn't find the EMBL retrieval client", embl);
     verifyProteinNucleotideXref(retrievalId, embl);
   }
 
+  /**
+   * Tests retrieval of one entry from EMBLCDS. Test is dependent on
+   * availability of network and the EMBLCDS service.
+   * 
+   * @throws Exception
+   */
   @Test(groups =
   { "External" })
   public void testEmblCDSUniprotProductRecovery() throws Exception
@@ -120,24 +143,46 @@ public class DbRefFetcherTest
     verifyProteinNucleotideXref(retrievalId, embl);
   }
 
+  /**
+   * Helper method to perform database retrieval and verification of results.
+   * 
+   * @param retrievalId
+   * @param embl
+   * @throws Exception
+   */
   private void verifyProteinNucleotideXref(String retrievalId,
           DbSourceProxy embl) throws Exception
   {
     AlignmentI alsq = embl.getSequenceRecords(retrievalId);
     assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
     assertEquals("Didn't retrieve right number of records", 1, alsq.getHeight());
-    DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
+    SequenceI seq = alsq.getSequenceAt(0);
+    assertEquals("Wrong sequence name", embl.getDbSource() + "|"
+            + retrievalId, seq.getName());
+    SequenceFeature[] sfs = seq.getSequenceFeatures();
+    assertNotNull("Sequence features missing", sfs);
+    assertTrue(
+            "Feature not CDS",
+            FeatureProperties.isCodingFeature(embl.getDbSource(),
+                    sfs[0].getType()));
+    assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
+    DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRef(), DBRefSource.PROTEINSEQ);
     assertNotNull(dr);
     assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
-    assertEquals("Expected cross refernce map to be one amino acid", dr[0]
+    assertEquals("Expected cross reference map to be one amino acid", dr[0]
             .getMap().getMappedWidth(), 1);
-    assertEquals("Expected local refernce map to be 3 nucleotides", dr[0]
+    assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
             .getMap().getWidth(), 3);
     AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
     assertNotNull(
             "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
             sprods);
-    
-    
+    assertEquals("Didn't xref right number of records", 1,
+            sprods.getHeight());
+    SequenceI proteinSeq = sprods.getSequenceAt(0);
+    assertEquals(proteinSeq.getSequenceAsString(), dr[0].getMap().getTo()
+            .getSequenceAsString());
+    assertEquals(dr[0].getSource() + "|" + dr[0].getAccessionId(),
+            proteinSeq.getName());
   }
 }